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H1-3 H1.3 linker histone, cluster member [ Homo sapiens (human) ]

Gene ID: 3007, updated on 5-Jul-2020

Summary

Official Symbol
H1-3provided by HGNC
Official Full Name
H1.3 linker histone, cluster memberprovided by HGNC
Primary source
HGNC:HGNC:4717
See related
Ensembl:ENSG00000124575 MIM:142210
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
H1D; H1.3; H1F3; H1s-2; HIST1H1D
Summary
Histones are basic nuclear proteins responsible for nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H1 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015]
Orthologs

Genomic context

See H1-3 in Genome Data Viewer
Location:
6p22.2
Exon count:
1
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (26234212..26234987, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (26234440..26235216, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3 clustered histone 6 Neighboring gene H2A clustered histone 9, pseudogene Neighboring gene H4 clustered histone 6 Neighboring gene H4 clustered histone 7

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Identification of ten loci associated with height highlights new biological pathways in human growth.
NHGRI GWA Catalog
Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify H1d associated HIV-1 Gag in 293T cells PubMed
Tat tat Overexpression of NPM1 enhances HIV-1 Tat-mediated transactivation by reducing the histone H1 occupancy on the chromatinized template of HIV-1 LTR PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC138176

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleosomal DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
chromosome condensation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K27 trimethylation IEA
Inferred from Electronic Annotation
more info
 
histone H3-K4 trimethylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of DNA recombination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of chromatin silencing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
nucleosome assembly IEA
Inferred from Electronic Annotation
more info
 
nucleosome positioning IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
host cell nucleus IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear euchromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear euchromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleosome IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
histone H1.3
Names
H1 histone family, member 3
histone 1, H1d
histone H1c
histone H1s-2
histone cluster 1 H1 family member d
histone cluster 1, H1d

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_005320.3NP_005311.1  histone H1.3

    See identical proteins and their annotated locations for NP_005311.1

    Status: REVIEWED

    Source sequence(s)
    AL031777
    Consensus CDS
    CCDS4597.1
    UniProtKB/Swiss-Prot
    P16402
    Related
    ENSP00000244534.5, ENST00000244534.6
    Conserved Domains (1) summary
    pfam00538
    Location:39109
    Linker_histone; linker histone H1 and H5 family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    26234212..26234987 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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